I know during the beta testing I was able to mod in 9 custom battle ships. But the retail version doesn't allow it that's a big let down.
Another thing is with carriers you may want to add more then the two default choices of fighter/bomber.
Haven't seen any resolution to this, not even Stardock has posted a reply to the previous posters.
I do not think there should be any limits on things like this it makes people not want to mod for the game and that would be a waste since sins is a pretty excellent game minus the things that were mentioned.
If this has already been answered please post a link here.